Both Darwinian and Lamarckian modalities of evolution appear to be important, and reflect different aspects of the interaction between populations and the environment.
Dr. Koonin is the author of “Sequence - Evolution – Function Computational Approaches in Comparative Genomics” (2003, with Michael Galperin) and “The Logic of Chance: The nature and origin of biological evolution” (2011). He is the founder and Editor-in-Chief (with Laura Landweber and David Lipman) of Biology Direct, an Open Access journal that also employs open peer-review. Dr. Koonin was elected Member of the American Academy of Microbiology, Fellow of the American College of Medical Informatics, Fellow of the American Academy of Arts and Sciences, Foreign Associate of the European Molecular Biology Organization, and Doctor Honoris Causa of Universite Aix-Marseille (France).
I) Empirical comparative and evolutionary genomics - comparison of prokaryotic and eukaryotic genomes with the aim of predicting gene functions, constructing evolutionary scenarios for particular gene families and functional categories, and deciphering general evolutionary trends. One of the products of this research direction is the database of Clusters of Orthologous Groups of proteins (COGs).
Ii) Exploitation of genome comparisons, particularly those between relatively close genomes, for addressing fundamental issues of evolutionary biology such as the nature of adaptation and selection in different categories of genes.
Auslander N, Wolf YI, Koonin EV. In silico learning of tumor evolution through mutational time series. Proc Natl Acad Sci U S A. 2019;116(19):9501-9510.
Iii) Classification and evolutionary analysis of protein domains and domain architectures. An important dimension in this type of research is the discovery of "new" domains that are shared by many diverse proteins but have not been defined previously.
Koonin EV, Krupovic M. Evolution of adaptive immunity from transposable elements combined with innate immune systems. Nat Rev Genet. 2015;16(3):184-92.
Dr. Koonin's group performs research in many areas of evolutionary genomics. The overall gist of Dr. Koonin's research is to take advantages of the advances of comparative genomics and systems biology to address fundamental problems in evolutionary biology.
The year 2009 is the 200th anniversary of the publication of Jean-Bapteste Lamarck’s Philosophie Zoologique and the 150th anniversary of Charles Darwin’s On the Origin of Species. Lamarck believed that evolution is driven primarily by non-randomly acquired, beneficial phenotypic changes, in particular, those directly affected by the use of organs, which Lamarck believed to be inheritable. In contrast, Darwin assigned a greater importance to random, undirected change that provided material for natural selection.
Shmakov S, Smargon A, Scott D, Cox D, Pyzocha N, Yan W, Abudayyeh OO, Gootenberg JS, Makarova KS, Wolf YI, Severinov K, Zhang F, Koonin EV. Diversity and evolution of class 2 CRISPR-Cas systems. Nat Rev Microbiol. 2017;15(3):169-182.